Nextflow workflow report

[determined_varahamihira]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER (Med1_VCAP_Daro_REP2)'

Caused by:
  Process `NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER (Med1_VCAP_Daro_REP2)` terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

  samtools view \
      -F 0x004 \
      -F 0x0400 \
      -q 1 \
      -L genome.include_regions.bed \
      -b Med1_VCAP_Daro_REP2.mLb.mkD.sorted.bam \
      | bamtools filter \
          -out Med1_VCAP_Daro_REP2.mLb.noPublish.bam \
          -script bamtools_filter_se.json
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
      bamtools: $(echo $(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /input/data/work/dd/583b0bb80a4b0f7ce2d9205cd06c13

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
22-Jan-2024 09:53:00 - 22-Jan-2024 20:26:03 (duration: 10h 33m 4s)
  1204 succeeded  
  0 cached  
  0 ignored  
  1 failed  
Nextflow command
nextflow run /input/chipseq -profile test_full -c /experiments/experiment/chipseq/nextflow.config -c /experiments/experiment/nextflow_cws.config -c /experiments/experiment/nextflow_ceph.config
CPU-Hours
268.9 (0% failed)
Launch directory
/experiments/experiment/launch
Work directory
/input/data/work
Project directory
/input/chipseq
Script name
main.nf
Script ID
73413072355e71512cca3175a986f037
Workflow session
f004f1a3-875e-41dd-b28f-3306a5358235
Workflow profile
test_full
Nextflow version
version 23.07.0-edge, build 5875 (28-07-2023 20:27 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

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(tasks table omitted because the dataset is too big)